|
| Status |
Public on Nov 02, 2018 |
| Title |
VEC_A_2 MPRA_control |
| Sample type |
SRA |
| |
|
| Source name |
C2C12
|
| Organism |
synthetic construct |
| Characteristics |
lncrna previous name: NA
background: NA
official strain name: NA
genotype: NA
Sex: NA
sample type: Vector DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryonic organs were harvested and homogenized in TRIzol. Cells were cultured and harvested directly in TRIzol.
Standard illumina protocols were used to make libraries (TruSeq RNA Sample Preparation Kit v2)
RNA-seq or plasmid-sequencing (For MPRA Vector DNA libraries)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
C2C12_lincmRNA_combined_Jan2017_hiseq.tab
|
| Data processing |
Custom python scripts were used to count barcodes in MPRA experiments.
In RNA seq experiments, reads were aligned to mm10 and quantified using rsem. For mESC samples, reads were first trimmed to 50bp.
Differential analysis was performed using DESeq
Genome_build: mm10
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Sep 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Abbie Groff |
| E-mail(s) |
agroff@fas.harvard.edu
|
| Organization name |
Harvard University
|
| Department |
Stem Cell and Regenerative Biology;
|
| Lab |
John Rinn
|
| Street address |
7 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL19604 |
| Series (1) |
| GSE104341 |
The Peril DNA locus acts as an in vivo enhancer for distal but not proximal genes |
|
| Relations |
| BioSample |
SAMN07710803 |
| SRA |
SRX3222752 |
